[EMBOSS] Embossdata -reject option

[pmr at ebi.ac.uk]

Mark Logghe wrote:

> I am intrigued by the -reject option of embossdata.
>
> I was not able to find out what this list of values corresponds to. I
> hoped to get a list to select from when embossdata was run with the
> -options parameter, but this did not happen.
> Any clues ?

Hmmmm .... yes, -help and the acdtable output (the table in the webpage
application documentation) really need to report the list of menu items
for values that are not prompted (list and selection datatypes).

We will do that for the next release!

Otherwise, you do need to look in the ACD file.

I propose:

-help to report documentation on the options
-help -verbose to report the list of options

acdtable to report the full menu formatted in the "Allowed values" box.

When this is implemented, it will appear in the apps/cvs/embossdata.html
documentation at emboss.sf.net :-)

>Yeah, that is of course the most obvious ;-) Thing is that I wanted to
>do it in an emboss-only way so that it would be possible to run the
>emboss command via a soaplab service. The latter should provide a means
>to dynamically fetch a list of codon usage tables. More or less like
>showdb is doing.

We are looking at ways to do that ... can be tricky if cutgextract has
been run. Any suggestions? A showdata application perhaps?

Hope that helps,

Peter